[Bioperl-l] FASTQ output

Hilmar Lapp hlapp at gmx.net
Sat Jul 4 09:49:39 EDT 2009

On Jul 1, 2009, at 5:48 AM, Chris Fields wrote:

> I am working on FASTQ output and noticed a real oddity.  Apparently,  
> there are three write_* methods for this module, with the odd choice  
> of write_seq for Bio::SeqIO::fastq writing FASTA, not FASTQ.   
> write_qual() writes Qual format:

Maybe the motivating thought was that a SeqIO module ought to write  
sequences when write_seq() is called. I agree though that a writer for  
a format ought to write that format and not something else.

> [...] is there a reason for duplicating output code for qual and  
> FASTA output within Bio::SeqIO::fastq

Hopefully not.

> [...]  Anyone have problems with me changing that up a bit?

Go ahead.

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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